From 52880329dfaf719975b5b6f0adf87710cc8e122e Mon Sep 17 00:00:00 2001
From: Toshiki Takeuchi <take@xcoo.jp>
Date: Thu, 20 Apr 2023 19:14:05 +0900
Subject: [PATCH 1/2] Prepare for next development iteration (0.4.7-SNAPSHOT)

---
 project.clj | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project.clj b/project.clj
index 53654e8..8143b7b 100644
--- a/project.clj
+++ b/project.clj
@@ -1,4 +1,4 @@
-(defproject clj-hgvs "0.4.6"
+(defproject clj-hgvs "0.4.7-SNAPSHOT"
   :description "Clojure(Script) library for handling HGVS"
   :url "https://github.com/chrovis/clj-hgvs"
   :license {:name "Apache License, Version 2.0"

From 017fe8512830eef1413fcc047f3ab6705d7db3b1 Mon Sep 17 00:00:00 2001
From: Toshiki Takeuchi <take@xcoo.jp>
Date: Thu, 20 Apr 2023 19:25:43 +0900
Subject: [PATCH 2/2] Fix format of uncertain protein mutation

---
 src/clj_hgvs/mutation.cljc       |  4 ++--
 test/clj_hgvs/mutation_test.cljc | 20 ++++++++++++++++----
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/src/clj_hgvs/mutation.cljc b/src/clj_hgvs/mutation.cljc
index e6311ff..5e2bd76 100644
--- a/src/clj_hgvs/mutation.cljc
+++ b/src/clj_hgvs/mutation.cljc
@@ -184,8 +184,8 @@
 (defrecord UncertainMutation [mutation]
   Mutation
   (format [this] (format this nil))
-  (format [this _]
-    (str "(" (format mutation) ")"))
+  (format [this opts]
+    (str "(" (format mutation opts) ")"))
   (plain [this]
     {:mutation "uncertain-mutation"
      :content-mutation (plain mutation)})
diff --git a/test/clj_hgvs/mutation_test.cljc b/test/clj_hgvs/mutation_test.cljc
index 23a158f..a49a292 100644
--- a/test/clj_hgvs/mutation_test.cljc
+++ b/test/clj_hgvs/mutation_test.cljc
@@ -39,17 +39,29 @@
 (def uncertain-mutation2 (mut/uncertain-mutation
                           (mut/rna-substitution (coord/rna-coordinate 306 nil nil) "g" "u")))
 
+(def uncertain-mutation3s "(Cys123Gly)")
+(def uncertain-mutation3ss "(C123G)")
+(def uncertain-mutation3k :protein)
+(def uncertain-mutation3 (mut/uncertain-mutation
+                          (mut/protein-substitution "Cys"
+                                                    (coord/protein-coordinate 123)
+                                                    "Gly")))
+
 (deftest format-uncertain-mutation-test
   (testing "returns a string expression of an uncertain mutation"
-    (are [m s] (= (mut/format m nil) s)
-      uncertain-mutation1 uncertain-mutation1s
-      uncertain-mutation2 uncertain-mutation2s)))
+    (are [m o s] (= (mut/format m o) s)
+      uncertain-mutation1 nil uncertain-mutation1s
+      uncertain-mutation2 nil uncertain-mutation2s
+      uncertain-mutation3 nil uncertain-mutation3s
+      uncertain-mutation3 {:amino-acid-format :short} uncertain-mutation3ss)))
 
 (deftest parse-uncertain-mutation-test
   (testing "returns a correct UncertainMutation"
     (are [s k m] (= (mut/parse-uncertain-mutation s k) m)
       uncertain-mutation1s uncertain-mutation1k uncertain-mutation1
-      uncertain-mutation2s uncertain-mutation2k uncertain-mutation2)))
+      uncertain-mutation2s uncertain-mutation2k uncertain-mutation2
+      uncertain-mutation3s uncertain-mutation3k uncertain-mutation3
+      uncertain-mutation3ss uncertain-mutation3k uncertain-mutation3)))
 
 (deftest plain-uncertain-mutation-test
   (testing "returns a plain map representing UncertainMutation"